HLA gene and haplotype frequencies in a Nagaybaks population from the Chelyabinsk Region (Russian South Urals).

A total of 112 Nagaybaks, a Turkic ethnoconfessional group living mainly in the Nagaybak district of the Chelyabinsk Region of Russian South Urals, were genotyped for HLA-A, -B, -DRB1, -DQA1 and -DQB1 loci using PCR-SSP (low-resolution) and HLA-A29 (high-resolution). All loci were in Hardy-Weinberg equilibrium (all p values >0.1 thus showing no locus-level deviations. The genotype data are available in the Allele Frequencies Net Database under the population name ''Russia, South Ural, Chelyabinsk Region, Nagaybaks" and the identifier AFND0003397.

Epitopes and motifs of the HLA-B*14 allele family products and related HLA-B14 cross-reactive specificities.

The split specificities of HLA-B14 (B64, B65) are assigned to the B*14:01 (B64) and B*14:02 (B65) products only. Of the further 50 B*14 expressed products, only B*14:03 and B*14:06 are officially designated as HLA-B14. The B*14:08 product differs from B64 by a single amino acid substitution of W97R, while the B*14:53 specificity (which is a "short" B14 and neither B64 nor B65) differs from B64 by three residues (W97S, Y113H and F116Y). Comprehensive testing of B*14:08:01 cells (using 49 alloantisera with B64 or B64, B65 specificities, and five monoclonal antibodies with B65 or B64, B65 activity) showed that the B*14:08 specificity is, like the B*14:53 product, neither B64 nor B65 and appears as a "short" B14 specificity. To help understand the serological reactivity of the B*14:08 and B*14:53 products, and B64 and B65, we identified seven published epitopes (11AV, 97W, 61ICT, 116F, 131S+163T, 170RH and 420) and, by inspection, 29 motifs, that encompass one or more of B64, B65 and various HLA-B14 cross-reactive group specificities. We then considered the possession of these epitopes and motifs by the products of B*14:01 to B*14:06, B*14:08 and B*14:53. Seventeen of the 29 motifs fully complied with the one-/two-patch functional epitope concept for amino acid proximity, as determined by Cn3D software, the remainder partially complied. The nature and patterns of epitopes and motifs possessed by both B*14:08 and B*14:53 specificities supported their designation as HLA-B14 but non-B64/B65. Also that epitope 97W, with 11S or 11A, is critical for serological B64 and B65 reactivity. And conversely, that epitope 116F, and several identified motifs, are probably unimportant for HLA-B14 antibody reactivity. The previous submission that the B*14:03 specificity is HLA-B65 was compatible with its epitope/motif pattern. B*14:04 cells would also be expected to react as B65, based on its epitope/motif pattern, and not as B64 as previously implied. Also, from their epitope/motif patterns, and external serological information, it is probable that the B*14:05 and B*14:06 specificities will both appear as "short" HLA-B14, non-B64/B65. Several epitopes and motifs encompassed a range of HLA-B specificities included in the serological HLA-B14 cross-reactive group, thus supporting these original serological findings.

The HLA-C*05 family allele - C*05:142.

The sequencing of exons 2-7 of a likely new HLA-C*05 allele identified the second example of HLA-C*05:142, in a male UK European, within a few months of the first example being found in Germany. C*05:142 differs from C*05:01:01:01 by a single base (395G>C) in exon 3 resulting in an amino acid substitution of R108P. Comprehensive serological HLA-Cw5 typing, using 19 antisera, indicated that C*05:142 encodes a "normal" Cw5 specificity. Failure to identify the involvement of position 108 in published HLA-C epitopes supported this assertion. The likely HLA class I C*05:142-bearing haplotype is A*02:01~C*05:142~B*44:02. This new allele has a maximum frequency of 0.00001, in 34,743 sequenced-based typed subjects, contrasting with that of C*05:01 (allele frequency 0.10441), in our local, largely UK European, blood donors.

HLA-A*24:374-A novel allele encoding the HLA-A2403 specificity.

HLA-A*24:374 differs from A*24:03:01:01 by 2 exon 3 bases resulting in a substitution of T163E.

Three new HLA alleles-B*49:43, C*03:321 and DQB1*02:72.

Immunogenetic information is provided on 3 novel HLA-B, -C and -DQB1 alleles.

A further HLA-DRB1*15 family allele - DRB1*15:112.

HLA-DRB1*15:112 differs from DRB1*15:01:01:01 by one base (282G > T) in exon 2 resulting in K65N.

Two new HLA class I alleles - A*11:241 and C*08:132.

HLA-A*11:241 differs from A*11:01:01:01 (215G > A, exon 2, R48Q); HLA-C*08:132 from C*08:02:01:01 (587 T > A exon 3, L172Q).

Five new HLA alleles with synonymous mutations: A*01:01:65, A*01:01:66, B*44:03:35, DRB1*15:01:30 and DQB1*02:01:24.

Immunogenetic information is provided on five novel alleles with synonymous mutations.

A novel HLA-B*14 allele - B*14:53 - genetics and serology.

HLA-B*14:53 was found in a UK European normal blood donor prior to registration on the Welsh Bone Marrow Donor Registry. It differs from B*14:13 by one base (103G>T) in exon 2 resulting in a substitution of alanine (A) in B*14:13 to serine (S) in B*14:53. Unique among current HLA-B*14 alleles, B*14:53 and B*14:13 share a motif of 59 bases between positions 361 and 419 in exon 3. This motif is present in numerous HLA-B alleles the commonest overall being B*08:01, suggesting that both B*14:53 and B*14:13 arose from intralocus gene conversion events with B*08:01. Thus, B*14:53 probably arose from B*14:01:01 (which has TCC at codon 11 (S), while B*14:13 arose from B*14:02:01:01 which has GCC at codon 11 (A). Additionally, the two likely B*14:53-bearing and B*14:13-bearing haplotypes are typical of B*14:01:01-bearing and B*14:02:01:01-bearing haplotypes, respectively. Serological testing, using 49 antisera with HLA-B64, or B64, B65 reactivity, showed that the B*14:53 specificity did not react as a B64 (B*14:01) specificity and may appear as a short/weak HLA-B14. This implies that residues additional to S at position 11 are involved in HLA-B64 serological identity; for example, the motif 11S 97W 116F is possessed by B*14:01 and many other B*14 products (and B*39:79 plus some HLA-C products) but not B65 (B*14:02) or the B*14:53 specificity. B*14:53 was found in a random HLA sequence-based typed population of 32 530 normal subjects indicating a low precision allele frequency of 0.000015 in subjects resident in Wales.

A further HLA-A*23 family allele--HLA-A*23:68.

HLA-A*23:68 differs from A*23:01:01 by one base (518C > A) in exon 3 resulting in an amino acid substitution of A149E.

Immunogenetics of three novel HLA-Class II alleles: DRB1*03:112, DQB1*03:02:16 and DQB1*03:139.

Three novel HLA-Class II alleles, DRB1*03:112, DQB1*03:02:16 and DQB1*03:139, are described with predicted bearing haplotypes of A*02:01, B*40:01, C*03:04, DRB1*03:112, DQB1*02:01; A*23:01, B*15:01, C*03:03, DRB1*04:01, DQB1*03:02:16 and A*01:01, B*44:02, C*05:01/03, DRB1*04:01, DQB1*03:139. Serological tests showed that the DRB1*03:112 and DQB1*03:139 specificities failed to react as expected with some well-documented monoclonal antibodies. Subsequent examination of published HLA-Class II epitopes and inspection of amino acid motifs suggested that epitopes exist that include the positions of their single substitutions (F31C between DRB1*03:01:01:01 and DRB1*03:112, and R48P between DQB1*03:01:01:01 and DQB1*03:139 specificities). This suggests that the reactivity of the monoclonal antibodies used was dependent on these epitopes and that their loss from these rare allele products resulted in their aberrant serology. The new alleles were found after the sequence-based typing of 32 530 random UK European routine blood donors suggesting that each has a maximum carriage frequency of 0.0031% in the blood donor population resident in Wales.

Three new HLA-DQB1 alleles ­ DQB1*03:113, DQB1*06:02:15 and DQB1*06:129.

Three novel HLA-DQB1 alleles were found after sequence-based typing of 3558 random UK European routine blood donors.

A new HLA-A*26 family allele--HLA-A*26:103.

HLA-A*26:103 differs from A*26:01:01 by one base (559C>G) in exon 3 resulting in an amino acid substitution of R163G.

A group-specific sequence-based typing approach for HLA-DQA1.

An HLA-DQA1 sequence-based typing method reliant upon group-specific amplification to achieve an unambiguous second-field DQA1 typing assignment is presented. Method validation, using 51 reference DNA samples covering 21 different DQA1 alleles, showed 100% concordance with the reference types. This typing strategy has several important uses including identifying DQA1 mismatches in kidney donor/recipient pairs to inform patient DQ antibody assignments.

Prevalence of HLA-DQA1 alleles and haplotypes in blood donors resident in Wales.

Two hundred and fifty-four normal blood donors, from a largely UK European population, were sequence-based typed for HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1 and HLA-DQB1. The fit to Hardy-Weinberg expectations was good for all loci (all P values >0.5). Fifteen DQA1 alleles were identified to the second field. DQA1 carriage, allele and DQA1-DQB1 and DRB1-DQA1-DQB1 haplotype frequencies, linkage disequilibria and related values are presented.

External quality assessment of patient HLA-B*57:01 testing prior to abacavir prescription.

Hypersensitivity reactions to the drug abacavir are strongly associated with possession of HLA-B*57:01. Hence, patients with HIV/AIDS who may be prescribed abacavir should be tested for this HLA allele and the drug withheld from those that possess B*57:01. The UK National External Quality Assessment Service for Histocompatibility and Immunogenetics has operated a scheme for B*57:01 testing since 2008 which, in 2013, involved 47 participants from 12 countries. A total of 24 B*57:01-positive, 2 B*57:03-positive and 22 B*57-negative blood samples (including 2 B*58 samples) were distributed to between 28 and 47 laboratories each year over 6 years. Participants, who were unaware of the samples' HLA types, tested and reported on their B*57/B*57:01 status. A total of 1868 reports were assessed over the 6 years. Of the 880 reports on B*57:01 samples, 93.4% were correctly assigned as B*57:01, 2.8% were assigned as groups of B*57 alleles including B*57:01, and 3.3% were reported as B*57 positive only. Over the 6 years, there were four (0.46%) false B*57:01 negative reports. All the B*57:03-positive and B*57-negative samples, involving 72 and 916 assignments, respectively, were essentially reported as B*57:01 negative. Thus, there were no false B57:01 positive assignments. The reporting of B*57:01 status over the last 3 years of the scheme was 99.8% sensitive and 100% specific. Over the last year, it was 100% sensitive and 100% specific.

A new HLA-A*01 allele - A*01:139.

HLA-A*01:139 differs from A*01:01:01:01 by one nucleotide (383G>C) resulting in an amino acid change of glycine104alanine.

A new HLA-A*03 null allele - A*03:162N caused by an exon 4 insertion and discovered during an external quality assessment exercise.

HLA-A*03:162N differs from A*03:01:01:01 by an exon 4, 664-665insCATG causing E198A and A199X.

HLA-B*27:05:25 - a further HLA-B*27:05 allele with a synonymous nucleotide substitution.

HLA-B*27:05:25 differs from B*27:05:02 by a single synonymous nucleotide substitution (192C>T) at codon 40 in exon 2.

16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report).

We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May-June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well-defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA-NET recommendations. The new data included, among others, large sets of well-defined populations from north-east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation-maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy-Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th-15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA-A, -B and -DRB1 loci but not for HLA-DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south-east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian-speaking South-East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.